This thread is really worth the time to read over. Seems like the Aprilia guys have it figured out.
http://www.apriliaforum.com/forums/showthread.php?34770-Water-Pump-Seals
One thing to note, is that from my understanding if you buy a clutch cover housing it comes with the seals already installed. So, to install the shaft you have to drive it through both seals (not good). This along with burs on the shaft as well as possible sloppy installation practices (using a hammer, haha...), can make the seal real prone to failure.
I figure I'll give the dealer one shot with it since mine is still under warranty. However, it really doesn't seem to be that big of a deal to do this repair correctly with just a little attention to detail....
Good Luck Guys!
Doug